k-dense-ai/scientific-agent-skills · skills/pathway-enrichment/SKILL.md

pathway-enrichment skillA

pathway-enrichment is agent-read markdown (skill) from k-dense-ai/scientific-agent-skills: Run pathway and gene-set enrichment analysis on gene lists or ranked gene data, then interpret the results. Use whenever the user has a set of genes (differentially expressed genes from PyDESeq2/Scanpy, CRISPR-screen hits, cluster marker genes, proteomics hits) and wants to know which biological pathways, GO terms, or gene sets are over-represented or enriched. Covers over-representation analysis (ORA / Enrichr / Fisher / hypergeometric), ranked Gene Set Enrichment Analysis (GSEA / preranked), s.

Indexed from public GitHub and served as immutable, content-addressed versions. Install it pinned to an exact SHA-256 with the mdr CLI, and every file is verified against the hash recorded here before it reaches your agent. The deterministic audit below grades the latest version, and the same file always earns the same grade.

How to install

Latest version
mdr add k-dense-ai/scientific-agent-skills/pathway-enrichment@v1.1
Exact content
mdr add k-dense-ai/scientific-agent-skills/pathway-enrichment@sha256:9738be9a8ba81124

Pin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.

Badge

mdr badge

[![mdr](https://markdownregistry.com/badge/art_v4od42wjuwr7uqsw.svg)](https://markdownregistry.com/a/art_v4od42wjuwr7uqsw)

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Versions

versioncommittedcommitsizeaudit
v1.1 latest2026-09-02 1e5eeff 13,590 BA view · diff
v1.02026-07-26 b085e11 12,632 BA view · diff
git:20260611.1b8fae32026-06-11 1b8fae3 12,637 BA view

Audit of the latest version

A  17 of 17 checks passed. Deterministic, no model, same answer every run.
  • pass: Frontmatter block present
  • pass: Frontmatter declares a name
  • pass: Frontmatter declares a description
  • pass: Size between 200 bytes and 200 KB (13590 bytes)
  • pass: No zero-width or bidi control characters
  • pass: No instruction hidden inside an HTML comment
  • pass: No link to an exfiltration or paste host
  • pass: No credential-shaped string
  • pass: No instruction to send local credentials anywhere
  • pass: No text hidden with inline styles
  • pass: No prompt-injection phrasing
  • pass: No curl or wget piped into a shell
  • pass: No recursive delete of root, home or parent
  • pass: No instruction to read or print local credentials
  • pass: No base64 blob over 200 characters
  • pass: No link to a raw IP address
  • pass: No script tag

Source

GitHub

k-dense-ai/scientific-agent-skills · 43,600 stars · license MIT · pushed 2026-09-07 · branch main

API

GET https://markdownregistry.com/api/v1/artifacts/art_v4od42wjuwr7uqsw
GET https://markdownregistry.com/api/v1/resolve?ref=k-dense-ai/scientific-agent-skills/pathway-enrichment
GET https://markdownregistry.com/api/v1/blob/9738be9a8ba8112410aed0fad1d8485c10e5188698f6737247c459022192d380